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Nonsyndromic Congenital Heart Disease Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
ACTC1 81405,81479
ACVR1 81479,81479
CHD7 81407,81479
CITED2 81479,81479
CRELD1 81479,81479
DCHS1 81479,81479
ELN 81479,81479
FLNA 81479,81479
FLT4 81479,81479
FOXF1 81479,81479
FOXH1 81479,81479
GATA4 81479,81479
GATA5 81479,81479
GATA6 81479,81479
GDF1 81479,81479
GJA1 81479,81479
HAND1 81479,81479
HAND2 81479,81479
JAG1 81407,81406
KDM6A 81479,81479
KMT2D 81479,81479
LEFTY2 81479,81479
MCTP2 81479,81479
MED13L 81479,81479
MEIS2 81479,81479
MYH11 81408,81479
MYH6 81407,81479
MYH7 81407,81479
NKX2-5 81479,81479
NKX2-6 81479,81479
NOTCH1 81407,81479
NOTCH2 81479,81479
NR2F2 81479,81479
PDGFRA 81479,81479
PITX2 81479,81479
PRDM6 81479,81479
SMAD6 81479,81479
TAB2 81479,81479
TBX1 81479,81479
TBX20 81479,81479
TBX5 81405,81479
TLL1 81479,81479
ZFPM2 81479,81479
ZIC3 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
13097Genes x (44)81479 81405(x2), 81406(x1), 81407(x5), 81408(x1), 81479(x79) $990 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Brett Deml, PhD

Clinical Features and Genetics

Clinical Features

Congenital heart disease (CHDs) encompasses a wide range of syndromic and non-syndromic conditions that feature structural abnormalities of the heart that arise during development. Nonsyndromic CHD is one of the most common birth defects and occurs in 1-3% of live births (Hoffman and Kaplan. 2002. PubMed ID: 12084585; van der Linde et al. 2011. PubMed ID: 22078432). Structural defects can include (but are not limited to): conotruncal abnormalities (tetralogy of Fallot, double-outlet right ventricle (DORV), truncus arteriosus, transposition of the great arteries (TGA), left ventricular outflow tract obstruction (coarctation of the aorta, aortic valve stenosis, bicuspid aortic valve, hypoplastic left heart), and septal defects. CHDs most commonly present as isolated structural defects of the heart; however, they can also present as part of a syndrome.

Recurrence risk for nonsyndromic CHDs is difficult to assess due to reduced penetrance, variable expressivity, environmental factors, and oligo/polygenic inheritance. Epidemiological studies suggest the recurrence risk for 1st degree relatives is ~3% and increases if a parent or two or more siblings are affected (5-10%) (Nora et al. 1994. PubMed ID: 8176108; Gill et al. 2003. PubMed ID: 12957444; Calcagni et al. 2007. PubMed ID: 17091259). However, recurrence risk varies by type of defect (Chaix et al. 2016. PubMed ID: 26981213) and is much higher in monogenic forms of CHDs.

Improved surgical and medical interventions has resulted in increasing prevalence of CHDs in adults. Determining the genetic etiology of CHDs allows for the identification of potential unanticipated extracardiac involvement, assess recurrence risk in future pregnancies, and can provide a more accurate prognosis.


CHDs can be inherited in an autosomal dominant (AD), autosomal recessive (AR), and X-linked (XL) manners. Nonsyndromic CHDs have been associated with both genetic (monogenic and oligo/polygenic) and environmental causes. Currently the genetic landscape of syndromic CHDs is better understood than nonsyndromic CHDs. Consistent with this, de novo variants have been found to contribute to ~8% of nonsyndromic CHD cases compared to 28% of CHD cases with extra cardiac anomalies (Jin et al. 2017. PubMed ID: 28991257; Homsy et al. 2015. PubMed ID: 26785492). The causes of monogenic forms of nonsyndromic CHDs are many and varied, but some of the most common include transcription factors important for heart development (NKX2-5, GATA4-6, HAND1, TBX1), notch signaling (JAG1, NOTCH1/2), and structural proteins (ACTC1, MYH7, ELN).  A wide range of genetic abnormalities, including aneuploidy (Down syndrome, Turner syndrome), chromosomal rearrangements, copy number variation (22q11.2 deletion syndrome, Williams-Beuren syndrome, Jacobsen syndrome, etc.), single nucleotide variants (SNVs), and insertions/deletions have been associated with CHDs.

See individual gene summaries for information about molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

The exact sensitivity of this panel is not known; however, sensitivity in nonsyndromic CHD is lower than syndromic forms. For isolated CHDs exome sequencing studies have found pathogenic variants in 16-20% of cases compared to 30-39% in syndromic forms (Alankarage et al. 2019. PubMed ID: 30293987; Shikany et al. 2020. PubMed ID: 32717230). Additionally, studies of large copy number variants (CNVs) using karyotype and chromosomal microarray have found pathogenic CNVs in ~6% of isolated cases compared to 26% in those with extra cardiac anomalies (Turan et al. 2018. PubMed ID: 29306563).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 98.1% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Please note that due to the presence of multiple pseudogenes, exons 1-4 of NOTCH2 are not covered by this test.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Patients with congenital heart defects are candidates for testing.


Name Inheritance OMIM ID
Adams-Oliver Syndrome 5 AD 616028
Alagille Syndrome 1 AD 118450
Alagille Syndrome 2 AD 610205
Alveolar Capillary Dysplasia With Misalignment Of Pulmonary Veins AD 265380
Aortic Aneurysm, Familial Thoracic 4 AD 132900
Aortic valve disease 2 AD 614823
Aortic Valve Disorder AD 109730
Atrial Septal Defect 2 AD 607941
Atrial Septal Defect 3 AD 614089
Atrial Septal Defect 4 AD 611363
Atrial Septal Defect 5 AD 612794
Atrial Septal Defect 6 AD 613087
Atrial septal defect 8 AD 614433
Atrial septal defect 9 AD 614475
Atrial Septal Defect With Atrioventricular Conduction Defects AD 108900
Atrioventricular Septal Defect AD 600309
Atrioventricular Septal Defect 2 AD 606217
Atrioventricular Septal Defect 4 AD 614430
Atrioventricular septal defect 5 AD 614474
Axenfeld-Rieger syndrome, type 1 AD 180500
Cardiac Valvular Dysplasia, X-Linked XL 314400
CHARGE Association AD 214800
Cleft palate, cardiac defects, and mental retardation AD 600987
Congenital heart defects, multiple types, 4 AD 615779
Congenital heart defects, multiple types, 5 AR 617912
Congenital heart defects, multiple types, 7 AD 618780
Congenital heart defects, nonsyndromic, 2 AD 614980
Conotruncal Heart Malformations AD 217095
Deafness, congenital heart defects, and posterior embryotoxon AD 617992
Digeorge Sequence AD 188400
Dilated Cardiomyopathy 1S AD 613426
Fallot Tetralogy AD 187500
Familial Hypertrophic Cardiomyopathy 1 AD 192600
Heterotaxy, Visceral, X-Linked XL 306955
Holt-Oram Syndrome AD 142900
Hypoplastic Left Heart Syndrome AR 241550
Hypoplastic Left Heart Syndrome 2 AD 614435
Iridogoniodysgenesis, Dominant Type AD 137600
Kabuki Syndrome 1 AD 147920
Kabuki Syndrome 2 XL 300867
Mental Retardation and Distinctive Facial Features with or without Cardiac Defects AD 616789
Mitral valve prolapse 2 AD 607829
Pancreatic agenesis and congenital heart defects AD 600001
Patent ductus arteriosus 3 AD 617039
Right atrial isomerism AR 208530
Supravalvar Aortic Stenosis AD 185500
Testicular Anomalies with or without Congenital Heart Disease AD 615542
Transposition Of Great Arteries AD 608808
Transposition Of The Great Arteries, Dextro-Looped 3 AD 613854
VACTERL Association With Hydrocephaly, X-Linked XL 314390
Velocardiofacial Syndrome AD 192430
Ventricular Septal Defect 1 AD 614429
Ventricular septal defect 2 AD 614431
Ventricular Septal Defect 3 AD 614432

Related Test

PGmaxTM - Comprehensive Congenital Heart Disease Panel


  • Alankarage et al. 2019. PubMed ID: 30293987
  • Calcagni et al. 2007. PubMed ID: 17091259
  • Chaix et al. 2016. PubMed ID: 26981213
  • Gill et al. 2003. PubMed ID: 12957444
  • Hoffman and Kaplan. 2002. PubMed ID: 12084585
  • Homsy et al. 2015. PubMed ID: 26785492
  • Jin et al. 2017. PubMed ID: 28991257
  • Nora et al. 1994. PubMed ID: 8176108
  • Shikany et al. 2020. PubMed ID: 32717230
  • Turan et al. 2018. PubMed ID: 29306563
  • van der Linde et al. 2011. PubMed ID: 22078432


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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